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Showing content from https://github.com/samtools/samtools/issues/2159 below:

merge gives warning on unsorted output but header says it is sorted · Issue #2159 · samtools/samtools · GitHub

Are you using the latest version of samtools and HTSlib? If not, please specify.

Yes (v1.21)

Please describe your environment. Please specify the steps taken to generate the issue, the command you are running and the relevant output.

When merging several BAM files with different headers, I get the warning message:

[bam_merge_core] Order of targets in file FILE1.bam caused coordinate sort to be lost

but the header of the output file still says it is sorted:

@HD     VN:1.5	SO:coordinate
[...]

shouldn't it be?

@HD     VN:1.5	SO:unsorted
[...]

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